A silsila is only as real as its documentation, and the instrument that makes a claimed chain verifiable is the ijaza, a written license a master issues to a disciple certifying that the transmission has been completed and naming the disciple as an authorized link in turn. Without one, a claim of initiation is a disciple's own assertion; with one, it is a credential other members of the order, and rival orders, can inspect, which is why historians of Sufism treat surviving ijazas as some of the clearest documentary evidence for how a given tariqa actually spread rather than how it later claimed to have spread.
The Naqshbandi order's chain through Abu Bakr rather than Ali is not a minor variant detail. Every other major tariqa traces its transmission through Ali ibn Abi Talib, even though the orders themselves are Sunni. Routing the chain instead through Abu Bakr, the first caliph and a figure whose primacy is a specifically Sunni claim, gave the Naqshbandiyya a genealogy that matched its doctrinal conservatism from its own founding narrative outward, rather than inheriting a structure built on a different line's account of legitimate succession.
A claim of Uwaysi transmission is harder to verify for exactly this reason: it reports instruction received without a living teacher and without any ijaza a rival order could ever inspect, which is precisely why Ahmad al-Tijani's use of it to found an independent line proved as controversial among other Sufi orders as it was foundational for his own.